Thanks. I have separated my initial mol2 file and I obtained two prepin
file. Then, I used the sequence command in leap to merge the two units
but the wrong tail and head atoms are taken. How can I manually define
these atoms? Thanks.
Best wishes,
Baptiste
Le 11/04/2011 18:32, Jason Swails a écrit :
> On Mon, Apr 11, 2011 at 7:29 AM, Baptiste Legrand<bap.legrand.gmail.com>wrote:
>
>> Dear all,
>>
>> I classically use amber and antechamber to solve NMR structures of
>> exotic molecules with repeated motifs. Nevertheless, for a molecule with
>> numerous motifs, I can't use antechamber because the molecule have 200+
>> atoms. So I generate a mol2 with Sirius (with the Gaff atom type) and
>> use the frcmod of the small molecules with identical motifs to start a
>> simulation. But the generated prmtop files in this case do not have
>> charges (zero) as my initial mol2 file do not have charges too.
>>
>> Is there a command in leap to calculate the charges as antechamber?
>> There is my typical script:
>>
> *calculate* the charges? No. leap doesn't calculate charges. Your best
> bet is to break up your system into residues and build charges for each of
> those residues independently. You can use R.E.D. tools for this.
>
> Good luck,
> Jason
>
>
>> #antechamber -i C4.mol2 -fi mol2 -o ./prep/C4.prepin -fo prepi -c bcc -s
>> 2> ./prep/antechamber.out
>> cat> leap.in<<EOF
>> source leaprc.gaff
>> source leaprc.ff99SB
>> UNK=loadmol2 C6.mol2
>> loadamberparams C4.frcmod
>> saveamberparm UNK ./prep/C6.prmtop ./prep/C6.inpcrd
>> quit
>> EOF
>> tleap -f leap.in> ./prep/leap.out
>>
>> Thanks,
>> Best wishes,
>> Baptiste
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Thu Apr 14 2011 - 11:00:04 PDT
